def _row_to_entry(row, corr_names, read_attrs):
oid = row[0]
name = row[1]
p_val = float(row[2])
corrections = {}
corrlist = row[3].split("|")
for i in xrange(len(corr_names)):
corrections[corr_names[i]] = float(corrlist[i])
entry = EnrichmentEntry(oid, name, p_val)
entry.corrections = corrections
if read_attrs and row[4]:
entry.attrs = ast.literal_eval(row[4])
return entry
def _row_to_entry(row, corr_names, read_attrs):
oid = row[0]
name = row[1]
p_val = float(row[2])
corrections = {}
corrlist = row[3].split("|")
for i in xrange(len(corr_names)):
corrections[corr_names[i]] = float(corrlist[i])
entry = EnrichmentEntry(oid, name, p_val)
entry.corrections = corrections
if read_attrs and row[4]:
entry.attrs = ast.literal_eval(row[4])
return entry
def test_read_correct(self):
inputstr = (
"# ranked parent-child\r\n"
"# 2 1\r\n"
"id\tname\tp-value\tbh_fdr|bonferroni\tattributes\r\n"
"9951\tstructure-specific DNA binding\t0.032301032301\t1.0|1.0\t{'plot': [0.1, 0.2, 1.0, 0.1], 'score': 1.0}\r\n"
"9916\tpolysomal ribosome\t0.025\t1.0|1.0\t\r\n"
"!\tCycles found...\r\n")
test_input = StringIO(inputstr)
e1 = EnrichmentEntry("9951", "structure-specific DNA binding",
0.032301032301)
e1.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e1.attrs = {'plot': [0.1, 0.2, 1.0, 0.1], 'score': 1.0}
e2 = EnrichmentEntry("9916", "polysomal ribosome", 0.025)
e2.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e2.attrs = {}
expected_en = Enrichment("ranked parent-child", [e1, e2],
["Cycles found..."], ['bh_fdr', 'bonferroni'])
reader = EnrichmentReader(test_input)
en = reader.read()
self.assertEqual(expected_en, en)
def test_write(self):
result = StringIO()
e1 = EnrichmentEntry("9951", "structure-specific DNA binding",
0.032301032301)
e1.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e1.attrs = {'plot': [0.1, 0.2, 1.0, 0.1]}
e2 = EnrichmentEntry("9916", "polysomal ribosome", 0.025)
e2.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e2.attrs = {}
en = Enrichment("ranked parent-child", [e1, e2], ["Cycles found..."],
['bh_fdr', 'bonferroni'])
writer = EnrichmentWriter(result)
writer.write(en)
expected = (
"# ranked parent-child\r\n"
"# 2 1\r\n"
"id\tname\tp-value\tbh_fdr|bonferroni\tattributes\r\n"
"9951\tstructure-specific DNA binding\t0.032301032301\t1.0|1.0\t{'plot': [0.1, 0.2, 1.0, 0.1]}\r\n"
"9916\tpolysomal ribosome\t0.025\t1.0|1.0\t{}\r\n"
"!\tCycles found...\r\n")
self.assertEqual(expected, result.getvalue())
def test_write(self):
result = StringIO()
e1 = EnrichmentEntry("9951", "structure-specific DNA binding", 0.032301032301)
e1.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e1.attrs = {'plot' : [0.1, 0.2, 1.0, 0.1]}
e2 = EnrichmentEntry("9916", "polysomal ribosome", 0.025)
e2.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e2.attrs = {}
en = Enrichment("ranked parent-child", [e1, e2], ["Cycles found..."], ['bh_fdr', 'bonferroni'])
writer = EnrichmentWriter(result)
writer.write(en)
expected = ("# ranked parent-child\r\n"
"# 2 1\r\n"
"id\tname\tp-value\tbh_fdr|bonferroni\tattributes\r\n"
"9951\tstructure-specific DNA binding\t0.032301032301\t1.0|1.0\t{'plot': [0.1, 0.2, 1.0, 0.1]}\r\n"
"9916\tpolysomal ribosome\t0.025\t1.0|1.0\t{}\r\n"
"!\tCycles found...\r\n")
self.assertEqual(expected, result.getvalue())
def test_read_correct(self):
inputstr = ("# ranked parent-child\r\n"
"# 2 1\r\n"
"id\tname\tp-value\tbh_fdr|bonferroni\tattributes\r\n"
"9951\tstructure-specific DNA binding\t0.032301032301\t1.0|1.0\t{'plot': [0.1, 0.2, 1.0, 0.1], 'score': 1.0}\r\n"
"9916\tpolysomal ribosome\t0.025\t1.0|1.0\t\r\n"
"!\tCycles found...\r\n")
test_input = StringIO(inputstr)
e1 = EnrichmentEntry("9951", "structure-specific DNA binding", 0.032301032301)
e1.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e1.attrs = {'plot' : [0.1, 0.2, 1.0, 0.1], 'score' : 1.0}
e2 = EnrichmentEntry("9916", "polysomal ribosome", 0.025)
e2.corrections = {'bh_fdr': 1.0, 'bonferroni': 1.0}
e2.attrs = {}
expected_en = Enrichment("ranked parent-child", [e1, e2], ["Cycles found..."], ['bh_fdr', 'bonferroni'])
reader = EnrichmentReader(test_input)
en = reader.read()
self.assertEqual(expected_en, en)
